Re: [galaxy-dev] configuring job runner slurm on cloudman
Hi, can someone tell me something about this? Pointing at the runner stated in the log vs. expected runner. Thanks, Alexander 2015-07-06 18:08 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com : Hi, I have adopted /mnt/galaxy/galaxy-app/config/job_conf.xml: I added a destination with following param: param id=nativeSpecification-N1 --cpus-per-task 1 --mem-per-cpu=4G/param Galaxy service was restarted after chaning this. Now I get the error Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. when I try to run a job. Looking in the log gives: galaxy.jobs.runners.drmaa DEBUG 2015-07-06 22:50:40,187 (493) submitting file /mnt/galaxy/tmp/job_working_directory/000/493/galaxy_493.sh galaxy.jobs.runners.drmaa DEBUG 2015-07-06 22:50:40,187 (493) native specification is: -N1 --cpus-per-task 1 --mem-per-cpu=4G galaxy.jobs.runners.drmaa ERROR 2015-07-06 22:50:40,187 (493) drmaa.Session.runJob() failed unconditionally Traceback (most recent call last): [...] InvalidAttributeValueException: code 14: Invalid native specification: -N1 --cpus-per-task 1 --mem-per-cpu=4G Well. running this as galaxy user in the console with $ srun -N1 --cpus-per-task 1 --mem-per-cpu=4G /mnt/galaxy/tmp/job_working_directory/000/494/galaxy_494.sh , it actually runs good. I was wondering if this is connected with the fact that the log states galaxy.jobs.runners.drmaa and not something like galaxy.jobs.runners.slurm, like defined in the job_conf.xml: plugin id=slurm type=runner load=galaxy.jobs.runners.slurm:SlurmJobRunner / So - What is going wrong here? Am I working on the wrong job_conf.xml? What does galaxy do here? Thanks for help!Alexander ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] August 2015 Galactic News
Hello all, The *August Galactic News https://wiki.galaxyproject.org/GalaxyUpdates/2015_08* is out. It's been a busy two months for the community. The *News* includes items on: - Events https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#Events: - *A report on the 2015 Galaxy Community Conference https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#GCC2015_Report* - *Details on the 2016 Galaxy Community Conference https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#GCC2016:_June_25-29.2C_2016.2C_Bloomington.2C_Indiana.2C_United_States* - August GalaxyAdmins Meetup https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#August_GalaxyAdmins_Meetup - July Pitagora-Galaxy Meetup https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#July_2015_Pitagora-Galaxy_Meetup - Other upcoming events https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#Other_Events - News of the, well, *new:* - 143 new papers, including 16 highlighted papers https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#New_Papers (this is what happens when you skip a month) - NGS 101 Tutorial Videos are Now Online https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#NGS_101_Tutorial_Videos_are_Now_Online - Genomic Data Science with Galaxy Launched on Coursera https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#Genomic_Data_Science_with_Galaxy_Launched_on_Coursera - Who's Hiring https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#Who.27s_Hiring - 5 new public Galaxy servers https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#New_Public_Galaxy_Servers (did I mention that we skipped a month?) - Community Committers! https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#Community_Committers.21 - 3 new Community Log Board entries, and 2 new teaching resources https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#Galaxy_Community_Hubs - New Releases https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#Releases of BioBlend https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#BioBlend_0.6.0_and_0.6.1 and Planemo https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#Planemo_0.13.0_through_0.13.2 - 76 Tool Shed updates and additions from 20+ contributors https://wiki.galaxyproject.org/ToolShed/Contributions/2015_07 - And, of course other news https://wiki.galaxyproject.org/GalaxyUpdates/2015_08#Other_News as well. Dave Clements and the Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] configuring job runner slurm on cloudman
I finally found out that this native specification is NOT about the native parameters of slurm. It comes from the DRMA-wrapper of slurm: http://apps.man.poznan.pl/trac/slurm-drmaa/wiki/WikiStart#Nativespecification And this does not support mem-per-cpu. Which is a huge restriction. The logger seems to print drmaa because it is the base class of the SlurmRunner. Anybody stumbled upon this before? A way would be to have a slurm runner that uses native calls instead of drmaa. Pros/Cons? Any opinions on this topic? Or solutions to get the mem-per-cpu option? I read, that this is criticised by some people from the slurm-drmaa community too. Patches are available, but not included in a release. Best, Alexander 2015-07-31 11:38 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com : Hi, can someone tell me something about this? Pointing at the runner stated in the log vs. expected runner. Thanks, Alexander 2015-07-06 18:08 GMT-05:00 Alexander Vowinkel vowinkel.alexan...@gmail.com: Hi, I have adopted /mnt/galaxy/galaxy-app/config/job_conf.xml: I added a destination with following param: param id=nativeSpecification-N1 --cpus-per-task 1 --mem-per-cpu=4G/param Galaxy service was restarted after chaning this. Now I get the error Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. when I try to run a job. Looking in the log gives: galaxy.jobs.runners.drmaa DEBUG 2015-07-06 22:50:40,187 (493) submitting file /mnt/galaxy/tmp/job_working_directory/000/493/galaxy_493.sh galaxy.jobs.runners.drmaa DEBUG 2015-07-06 22:50:40,187 (493) native specification is: -N1 --cpus-per-task 1 --mem-per-cpu=4G galaxy.jobs.runners.drmaa ERROR 2015-07-06 22:50:40,187 (493) drmaa.Session.runJob() failed unconditionally Traceback (most recent call last): [...] InvalidAttributeValueException: code 14: Invalid native specification: -N1 --cpus-per-task 1 --mem-per-cpu=4G Well. running this as galaxy user in the console with $ srun -N1 --cpus-per-task 1 --mem-per-cpu=4G /mnt/galaxy/tmp/job_working_directory/000/494/galaxy_494.sh , it actually runs good. I was wondering if this is connected with the fact that the log states galaxy.jobs.runners.drmaa and not something like galaxy.jobs.runners.slurm, like defined in the job_conf.xml: plugin id=slurm type=runner load=galaxy.jobs.runners.slurm:SlurmJobRunner / So - What is going wrong here? Am I working on the wrong job_conf.xml? What does galaxy do here? Thanks for help!Alexander ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable
Hi, My question is to the docker-galaxy-stable community. I would like to use or extend this image with some Galaxy settings externalized. For instance, I would like to define my own GALAXY_UID and GALAXY_HOME environment variables. I have tried the -e setting when I build and run the container, but that doesn't work: docker run -d -p 8080:80 -p 8021:21 -e GALAXY_UID=1777 -e GALAXY_HOME=/home/galaxy/env_test --name galaxy-env-test bgruening/galaxy-stable ... docker exec -ti galaxy-env-test bash # getent passwd galaxy galaxy:x:1450:1450:Galaxy user:/home/galaxy: As you can see from above, GALAXY_UID is 1450, as hardcoded in the Dockerfile, and not 1777, as I've specified. Same goes for the home directory. Is there any other way that I can set those variables? If not, what would be the best way to proceed, since, ideally, I would like to extend the galaxy-stable Docker image, and not change the existing one. Currently, I don't see any other way but to fork https://github.com/bgruening/docker-galaxy-stable and change the Dockerfile to externalize those (and other) variables. I hope I can get better suggestions than this. Cheers, Oksana ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
